bigMap::ptsne
# read dataset file
D <- read.csv('~/omics/10xmouse/10x1M.csv')
# get labels
L <- as.numeric(as.factor(D[, 52]))
# define a bigMap generic instance to perform ptSNE on a HPC
# note: data is passed as the name of a .csv file with input data
m <- bdm.init('10x1M', '~/omics/10xmouse/10x1M.csv.gz')
perplpexity 50
# bigMap::ptsne; run on HPC platform
m.50 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 50)
# bigMap::k-ary-neihgbourhood preservation; run on HPC platform
m.50 <- bdm.qlty(m.50, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
# transfer to local machine
bdm.scp(m.50)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p50.RData
perplpexity 100
m.100 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 100)
m.100 <- bdm.qlty(m.100, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
bdm.scp(m.100)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p100.RData
perplpexity 200
m.200 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 200)
m.200 <- bdm.qlty(m.200, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
bdm.scp(m.200)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p200.RData
perplpexity 400
m.400 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 400)
m.400 <- bdm.qlty(m.400, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
bdm.scp(m.400)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p400.RData
perplpexity 800
m.800 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 800)
m.800 <- bdm.qlty(m.800, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
bdm.scp(m.800)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p800.RData
perplpexity 1600
m.1600 <- bdm.ptsne(m, threads = 100, type = 'MPI', layers = 2, boost = 3, ppx = 1600)
m.1600 <- bdm.qlty(m.1600, inp.data = '~/omics/10xmouse/10x1M.csv.gz', threads = 60, type = 'SOCK', layers = 2, ret.qlty = T, qm = 'kn')
bdm.scp(m.1600)
+++ saved to ~/omics/10xmouse/10x1M_z100_l2_b3_r1_p1600.RData